diff find_str.py @ 1:1085e094cf5f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/find_str.py	Sat Jul 13 12:39:06 2024 +0000
@@ -0,0 +1,99 @@
+import argparse
+
+import pytrf  # 1.3.0
+from pyfastx import Fastx  # 0.5.2
+
+"""
+Allows all STR or those for a subset of motifs to be written to a bed file
+Designed to build some of the microsatellite tracks from https://github.com/arangrhie/T2T-Polish/tree/master/pattern for the VGP.
+"""
+
+
+def write_ssrs(args):
+    """
+    The integers in the call change the minimum repeats for mono-, di-, tri-, tetra-, penta-, hexa-nucleotide repeats
+    ssrs = pytrf.STRFinder(name, seq, 10, 6, 4, 3, 3, 3)
+    NOTE: Dinucleotides GA and AG are reported separately by https://github.com/marbl/seqrequester.
+    The reversed pair STRs are about as common in the documentation sample.
+    Sequence read bias might be influenced by GC density or some other specific motif.
+    """
+    bed = []
+    specific = None
+    if args.specific:
+        specific = args.specific.upper().split(",")
+    fa = Fastx(args.fasta, uppercase=True)
+    for name, seq in fa:
+        if args.specific:
+            ssrs = pytrf.STRFinder(
+                name,
+                seq,
+                args.minreps,
+                args.minreps,
+                args.minreps,
+                args.minreps,
+                args.minreps,
+                args.minreps,
+            )
+        else:
+            ssrs = pytrf.STRFinder(
+                name,
+                seq,
+                args.monomin,
+                args.dimin,
+                args.trimin,
+                args.tetramin,
+                args.pentamin,
+                args.hexamin,
+            )
+        for ssr in ssrs:
+            row = (
+                ssr.chrom,
+                ssr.start - 1,
+                ssr.end,
+                ssr.motif,
+                ssr.repeat,
+                ssr.length,
+            )
+            # pytrf reports a 1 based start position so start-1 fixes the bed interval lengths
+            if args.specific and ssr.motif in specific:
+                bed.append(row)
+            elif args.mono and len(ssr.motif) == 1:
+                bed.append(row)
+            elif args.di and len(ssr.motif) == 2:
+                bed.append(row)
+            elif args.tri and len(ssr.motif) == 3:
+                bed.append(row)
+            elif args.tetra and len(ssr.motif) == 4:
+                bed.append(row)
+            elif args.penta and len(ssr.motif) == 5:
+                bed.append(row)
+            elif args.hexa and len(ssr.motif) == 6:
+                bed.append(row)
+    bed.sort()
+    obed = ["%s\t%d\t%d\t%s_%d\t%d" % x for x in bed]
+    with open(args.bed, "w") as outbed:
+        outbed.write("\n".join(obed))
+        outbed.write("\n")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    a = parser.add_argument
+    a("--di", action="store_true")
+    a("--tri", action="store_true")
+    a("--tetra", action="store_true")
+    a("--penta", action="store_true")
+    a("--hexa", action="store_true")
+    a("--mono", action="store_true")
+    a("--dimin", default=2, type=int)
+    a("--trimin", default=2, type=int)
+    a("--tetramin", default=2, type=int)
+    a("--pentamin", default=2, type=int)
+    a("--hexamin", default=2, type=int)
+    a("--monomin", default=2, type=int)
+    a("-f", "--fasta", default="humsamp.fa")
+    a("-b", "--bed", default="humsamp.bed")
+    a("--specific", default=None)
+    a("--minreps", default=2, type=int)
+    args = parser.parse_args()
+    write_ssrs(args)